Recently discovered light-driven Na pumps are novel optogenetic tools. Activated by light, they actively transport Na outward across cell membrane. However, the mechanism of Na transport remains elusive. Visible absorption spectra, fluorescence spectra and ITC results of NdR2, a light-driven Na pump, indicated that Na may not bind to NdR2 in the ground state. Moreover, Na transport kinetics and functional assay suggested that Na transport might be altered at acidic pH. This pH-dependent transport of Na may shed light on and the mechanism of Na transport in NaRs.